Children walking home from school in the gold mining town of Mongbwalu, Democratic Republic of Congo. In the DRC, many girls are kept from school. Photograph: Spencer Platt/Getty Images

The United Nations today accuses world leaders of "turning a blind eye" to systematic rape in conflict countries as it calls for those responsible to be charged by the international criminal court (ICC) in the Hague.

Unesco says that in 35 countries affected by conflict there are 28 million children out of school, 42% of the world total. Wars also lead to some of the biggest inequalities between girls and boys in school enrolment, while child malnutrition levels are twice the average for developing nations.

"The neglect and inertia demonstrated by the international community is almost as shocking as the crimes themselves," says Kevin Watkins, the lead author of the report. "In effect, world leaders are turning their backs on young girls who desperately need protection, and turning a blind eye to crimes against humanity." He urges the UK government, which he says has been largely silent on the issue, to follow the lead of US secretary of state, Hillary Clinton, and put the prevention of rape and sexual violence in conflict-affected states at the centre of its foreign-policy agenda.

The report calls for the creation of an International Commission on Rape and Sexual Violence to investigate countries identified as centres of impunity, with the dossier passed directly to the ICC to determine whether there are grounds for prosecution. "Without prejudging outcomes of due legal process, there is no doubt that many senior political and military leaders, as well as armed militia leaders, in countries such as Chad, Sudan and the Democratic Republic of Congo [DRC] might anticipate early receipt of an ICC arrest warrant," Watkins says.

Unesco says the impact of rape and sexual violence on girls' education has been underestimated. For the immediate victims, physical injury and psychological trauma has long-term consequences, including acute depression, stigma and isolation. But the threat posed by rape also means many parents are unwilling to allow girls to make the journey to school. In North Kivu province of the DRC, one of the rape capitals of the world, almost half of 17- to 22-year-old women received less than two years of education.

"This is a hidden crisis that is reinforcing poverty, undermining economic growth and holding back the progress of nations," the report says. "At the heart of the crisis are widespread and systematic human rights violations which fully deserve to be called 'barbarous acts'. No issue merits more urgent attention on the international agenda. Yet, far from outraging the conscience of humankind and galvanising an effective response, the devastating effects of warfare on education go largely unreported.

"There is a culture of impunity surrounding egregious violations of human rights which represents a major barrier to education. Attacks on children, teachers and schools, and recourse to widespread and systematic rape and other forms of sexual violence as a weapon of war are among the starkest examples of such violations."

Other attacks on education systems cited by Unesco include Israeli military attacks in Gaza, which left almost 300 schools in rubble and 350 children dead, and targeted attacks by insurgents in countries such as Yemen, Thailand, Pakistan and Afghanistan. In Afghanistan, security fears have resulted in the closure of more than 70% of schools in Helmand and Zabul provinces in Afghanistan.

The report highlights the way in which aid to conflict-affected countries is skewed towards states seen as strategic priorities. Afghanistan receives more aid than the combined total for the DRC, Sudan and Liberia. In 2008, Iraq got more aid than that provided for all conflict-affected countries in Africa.

Unesco says 21 of the world's poorest countries spend more on arms than basic education, noting that a 10% cut in military spending could put an additional 9.5 million children in school. With some of the worst education indicators in the world, Chad spent four times as much on the military as on schooling, while Pakistan, which has one of the world's largest out-of-school populations, could finance universal primary education with just one-fifth of its military budget.

The report calls on donors to increase support for countries emerging from conflict by pooling their resources. It urges a radical financial overhaul of the Fast Track Initiative, a multilateral fund for education operating under World Bank auspices, with financing increased from $500m (£310m) to $6bn annually and a stronger focus on conflict-affected countries.

According to the 2011 Unesco Education for All global monitoring report:

• An additional 52 million children enrolled in primary school between 1999 and 2008

• The number of children out of school in south and west Asia halved. In sub-Saharan Africa enrolment rose by a third

• Progress towards universal enrolment by 2015 has slowed. In 2008, 67 million children were out of school

• Another 1.9 million teachers will be needed by 2015 to achieve universal primary education, more than half of them in sub-Saharan Africa

• The financial crisis has affected spending on education by poor countries. Seven of the 18 countries surveyed by Unesco had reduced their budgets

• Aid spending by donor countries has doubled since 2002 to $4.7bn but has stagnated since 2007.